Add ICONCLASS source (#433)

Closes #432

Author: cthoyt

src/pyobo/sources/__init__.py

@@ -34,6 +34,7 @@
 from .hgnc import HGNCGetter, HGNCGroupGetter
 from .iana_media_type import IANAGetter
 from .icd import ICD10Getter, ICD11Getter
+from .iconclass import IconclassGetter
 from .intact import IntactGetter
 from .interpro import InterProGetter
 from .itis import ITISGetter
@@ -115,6 +116,7 @@
     "ICD10Getter",
     "ICD11Getter",
     "ITISGetter",
+    "IconclassGetter",
     "IntactGetter",
     "InterProGetter",
     "KEGGGeneGetter",

src/pyobo/sources/chembl/chembl_target.py

@@ -138,7 +138,7 @@ def iter_terms(version: str) -> Iterable[Term]:
 def get_chembl_protein_equivalences(version: str | None = None) -> dict[str, list[str]]:
     """Get ChEMBL protein equivalences."""
     if version is None:
-        version = chembl_downloader.latest()
+        version = chembl_downloader.latest(full=False)
     url = f"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_{version}/chembl_uniprot_mapping.txt"
     df = ensure_df(
         PREFIX,

src/pyobo/sources/iconclass.py

@@ -0,0 +1,55 @@
+"""Get ICONCLASS as OBO."""
+
+from collections.abc import Iterable
+from urllib.parse import quote
+
+import pandas as pd
+
+from pyobo.struct import Obo, Term
+from pyobo.utils.path import ensure_df
+
+__all__ = [
+    "IconclassGetter",
+]
+
+PREFIX = "iconclass"
+BASE_URL = "https://github.com/iconclass/data/raw/refs/heads/main/txt/en/txt_en_{}.txt"
+URLS = [
+    BASE_URL.format("0_1"),
+    BASE_URL.format("2_3"),
+    BASE_URL.format("4"),
+    BASE_URL.format("5_6_7_8"),
+    BASE_URL.format("9"),
+    BASE_URL.format("keys"),
+    # shakespeare
+]
+
+
+def get_df() -> pd.DataFrame:
+    """Get an ICONCLASS terms dataframe."""
+    df = pd.concat(
+        ensure_df(prefix=PREFIX, url=url, sep="|", names=["luid", "name"]) for url in URLS
+    )
+    return df
+
+
+def iter_terms() -> Iterable[Term]:
+    """Iterate over terms in ICONCLASS."""
+    for luid, name in get_df().values:
+        yv = Term.from_triple(prefix=PREFIX, identifier=quote(luid), name=name)
+        yield yv
+
+
+class IconclassGetter(Obo):
+    """An ontology representation of ICONCLASS."""
+
+    ontology = PREFIX
+    dynamic_version = True
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iter_terms()
+
+
+if __name__ == "__main__":
+    IconclassGetter.cli()

tests/test_struct/test_obo/test_typedef.py

@@ -835,7 +835,7 @@ def test_32_relationship(self) -> None:
 
     def test_33_is_obsolete(self) -> None:
         """Test the ``is_obsolete`` tag."""
-        td_true, td_false = self.assert_boolean_tag("is_obsolete", funowl_curie="owl:deprecated")
+        self.assert_boolean_tag("is_obsolete", funowl_curie="owl:deprecated")
 
     def test_34_created_by(self) -> None:
         """Test the ``created_by`` tag."""